If you then save the annotated snapshot to your Downloads folder, you could use ZotFile's "Attach New File" function as explained above.

Re comment by zmetedlinler, does this approach allow you to annotate the pdf (highlight and then save) and then extract with zotfile?

Thank you for your responses. In order to have consistent workflow, I would like to have pdfs from academic journals and articles from websites amenable to annotation and extraction with zotfile. I

it and then extract it using something like zotfile. the above message (December 8, 2020) is the most recent comment on this issue. The following seperate discussions end with the same comment date

My bad, I thought I have the files/attachments stored with Zotero, but it was with Zotfile. Re-moved everything to the new disk and voila... I was indeed looking in the wrong place...

=> Zotero PMCID fetcher (0.0.11, extension), ZotFile (5.0.16, extension), Zotero Memento (1.0.0, extension), Zotero Storage Scanner (5.0.8, extension), Zotero Citation Counts Manager (1.1.0, extensio

I had Zotero installed in PC1, with Zotfile custome location of my pdfs set to /home/USER/Dropbox/zotero-library

Zotfile hasn't been updated to work with the new PDF Reader, and you should generally assume that all of its file moving and note-related functionality will be broken with it.

I was still using the zotfile extract annotations despite the new pdf reader beta as I had altered the configuration preferences to output something a bit more aesthetically pleasing (from here: https

It gets lost because under the hood Zotfile deletes the attachment item and makes a new one. Zotfile hasn’t been updated to accommodate the new PDF reader, and updating it would likely require a major

Sorry, I meant the highlighted text. The annotations do export fine with the built-in option. But if I rename/move a PDF using ZotFile (Manage attachments > Rename attachments), it seems to get rid of

The ZotFile part sounds like a misunderstanding:

You're totally right, I'm still new to Zotero and was getting its functionalities mixed with Zotfile.

Okay, it’s great that it will be possible at some point, just for interoperability reasons to work seamlessly between platforms, because Zotfile doesn’t seem to be able to extract the new annotations

You don't need ZotFile to extract Zotero annotations into a note (and ZotFile doesn't know anything about those, since it hasn't been updated). You can create a note from Zotero annotations by right-c

When I extract annotations from my files, Zotfile does fine with the underline I've done in the Xodo reader I use on my tablet on the pdf files. However, whenever I highlight in the Zotero integrated

@dstillman: Hmm. However, Zotfile does not recognise the notes and markings created "internally" in this way either. Is there an alternative?

I coded a JS to clean the customized reference fold after Zotfile is installed, https://github.com/redleafnew/zotero-javascripts/blob/main/4delete the attachment files after the items have been remove

I'm using ZotFile to extract annotations/highlighted text from PDFs to notes. I would like to use this information in mind maps including the possibility to use the reference link from within Freeplan

irrelevant? I want to go through the automated zotfile process of rename and move but I don't want to lose potentially valuable data I could manually parse myself later.